Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications
The haptophyte Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains in...
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Frontiers Media S.A.
2021-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.676447/full |
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| author | Huiyin Song Huiyin Song Huiyin Song Yang Chen Yang Chen Yang Chen Yang Chen Feng Liu Feng Liu Feng Liu Nansheng Chen Nansheng Chen Nansheng Chen Nansheng Chen |
| author_facet | Huiyin Song Huiyin Song Huiyin Song Yang Chen Yang Chen Yang Chen Yang Chen Feng Liu Feng Liu Feng Liu Nansheng Chen Nansheng Chen Nansheng Chen Nansheng Chen |
| author_sort | Huiyin Song |
| collection | DOAJ |
| description | The haptophyte Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains incomplete due to its long repeat sequences. In this study, we constructed the first full-length mtDNA of P. globosa, which was a circular genome with a size of 43,585 bp by applying the PacBio single molecular sequencing method. The mtDNA of this P. globosa strain (CNS00066), which was isolated from the Beibu Gulf, China, encoded 19 protein-coding genes (PCGs), 25 tRNA genes, and two rRNA genes. It contained two large repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions, which were missing from the previous mtDNA assembly, accounted for almost half of the entire mtDNA and represented the longest repeat region among all sequenced haptophyte mtDNAs. In this study, we tested the hypothesis that repeat unit amplification is a driving force for different mtDNA sizes. Comparative analysis of mtDNAs of five additional P. globosa strains (four strains obtained in this study, and one strain previously published) revealed that all six mtDNAs shared identical numbers of genes but with dramatically different repeat regions. A homologous repeat unit was identified but with hugely different numbers of copies in all P. globosa strains. Thus, repeat amplification may represent an important driving force of mtDNA evolution in P. globosa. |
| first_indexed | 2024-12-20T22:18:34Z |
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| id | doaj.art-f5351df4f23348f4b1df40e06c74df78 |
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| language | English |
| last_indexed | 2024-12-20T22:18:34Z |
| publishDate | 2021-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-f5351df4f23348f4b1df40e06c74df782022-12-21T19:24:59ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-07-011210.3389/fmicb.2021.676447676447Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat AmplificationsHuiyin Song0Huiyin Song1Huiyin Song2Yang Chen3Yang Chen4Yang Chen5Yang Chen6Feng Liu7Feng Liu8Feng Liu9Nansheng Chen10Nansheng Chen11Nansheng Chen12Nansheng Chen13CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, ChinaLaboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaCenter for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, ChinaLaboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaCenter for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, ChinaSchool of Earth and Planetary, University of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, ChinaLaboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaCenter for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, ChinaLaboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaCenter for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, ChinaDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, CanadaThe haptophyte Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains incomplete due to its long repeat sequences. In this study, we constructed the first full-length mtDNA of P. globosa, which was a circular genome with a size of 43,585 bp by applying the PacBio single molecular sequencing method. The mtDNA of this P. globosa strain (CNS00066), which was isolated from the Beibu Gulf, China, encoded 19 protein-coding genes (PCGs), 25 tRNA genes, and two rRNA genes. It contained two large repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions, which were missing from the previous mtDNA assembly, accounted for almost half of the entire mtDNA and represented the longest repeat region among all sequenced haptophyte mtDNAs. In this study, we tested the hypothesis that repeat unit amplification is a driving force for different mtDNA sizes. Comparative analysis of mtDNAs of five additional P. globosa strains (four strains obtained in this study, and one strain previously published) revealed that all six mtDNAs shared identical numbers of genes but with dramatically different repeat regions. A homologous repeat unit was identified but with hugely different numbers of copies in all P. globosa strains. Thus, repeat amplification may represent an important driving force of mtDNA evolution in P. globosa.https://www.frontiersin.org/articles/10.3389/fmicb.2021.676447/fullmtDNA sizesmitochondrial genomesPhaeocystis globosarepeat regionHaptophyta |
| spellingShingle | Huiyin Song Huiyin Song Huiyin Song Yang Chen Yang Chen Yang Chen Yang Chen Feng Liu Feng Liu Feng Liu Nansheng Chen Nansheng Chen Nansheng Chen Nansheng Chen Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications Frontiers in Microbiology mtDNA sizes mitochondrial genomes Phaeocystis globosa repeat region Haptophyta |
| title | Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications |
| title_full | Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications |
| title_fullStr | Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications |
| title_full_unstemmed | Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications |
| title_short | Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications |
| title_sort | large differences in the haptophyte phaeocystis globosa mitochondrial genomes driven by repeat amplifications |
| topic | mtDNA sizes mitochondrial genomes Phaeocystis globosa repeat region Haptophyta |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.676447/full |
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